MERFISH Report

1. Overview

1.1 Sample Information

A brief sample information is generated from the submission table for the following analysis.

Sample Index and Basic Information
Batch Index Data Path region
1 1 202402271312_20240227WenhaoAAVPanNeuro500mTriFx04_VMSC05201WH region_0
1 2 202402271312_20240227WenhaoAAVPanNeuro500mTriFx04_VMSC05201WH region_1
1 3 202402271312_20240227WenhaoAAVPanNeuro500mTriFx04_VMSC05201WH region_2

1.2 MERSCOPE Data Quality Summary

The summaries present the data quality assessment automatically generated by MERSCOPE for each experiment. We mainly focus on the transcripts level for each sample. So we’re looking for high density in transcripts, based on the transcripts count per field of view (FOV), transcript density in FOV, and frequency of transcripts detected.

Need to note that the low accuracy in DAPI cell boundary is not a concern, as a self-designed cell segmentation processing will take over this task.

MERSCOPE Data Quality Summary

MERSCOPE Data Quality Summary

MERSCOPE Data Quality Summary

MERSCOPE Data Quality Summary

MERSCOPE Data Quality Summary

MERSCOPE Data Quality Summary

2. Data Processing & Analysis

2.1 Cell Segmentation

Based on the spatial information and images obtained from MERFISH, we developed a machine learning model using the Cellpose algorithm to distinguish individual cells via MERFISH DAPI images.

To ensure the data quality and accuracy of cells, we have defined the minimum and maximum values for cell volume and gene count per cell. The cell volume should be between [100, 1800], and the gene count per cell > 25. After filter the outliers, the qualified cells count is shown in the following table.

Outliers were filtered from the data, and the qualified cells count is presented in the following table. The identified cells after filtering are listed in the following table. In total, the study identified 219765 cells across 4 samples.

Segmented Cell Count in each Samples
Sample Index Cell Count
region_1/ 16714
region_2/ 15800
region_0/ 11117
Identified Cell Spatial Overview on all Samples

Identified Cell Spatial Overview on all Samples

2.2 Dimension Reduction

We use Scanpy for the analysis of single-cell level transcriptome data.

Leiden Umap can be dividied to 28 clusters

Leiden Umap can be dividied to 28 clusters

2.3 Cell Annotation

We use a recent published tool: Map My Cell to perform cell type annotations for each cell. It is a high resolution cell type annotator build by Alan Institude, with nested levels of classification including 34 classes and 338 subclasses.

The taxonomy is based on the Allen Mouse Brain Common Coordinate Framework version 3 (CCFv3). Part of the used abbreviations is list in the supplementary Abbreviation. Otherwise can be found in CCFv3 paper.

With the annotation, we can identify and plot the selected types of cells in each sample.

2.3.1 Cell Annotation (Low resolution class)

MapMyCell Annotation Cell Count (Low resolution class)
class_name count
4 01 IT-ET Glut 15093
7 02 NP-CT-L6b Glut 5284
20 30 Astro-Epen 4858
11 20 MB GABA 3352
28 19 MB Glut 2557
6 07 CTX-MGE GABA 1961
0 06 CTX-CGE GABA 1310
13 31 OPC-Oligo 1194
15 18 TH Glut 1069
10 34 Immune 1037
9 12 HY GABA 653
23 33 Vascular 626
17 24 MY Glut 552
12 27 MY GABA 522
14 21 MB Dopa 517
8 04 DG-IMN Glut 439
16 05 OB-IMN GABA 382
18 26 P GABA 352
24 23 P Glut 273
21 28 CB GABA 249
3 11 CNU-HYa GABA 245
29 14 HY Glut 238
5 13 CNU-HYa Glut 180
2 08 CNU-MGE GABA 135
19 17 MH-LH Glut 92
22 29 CB Glut 77
27 09 CNU-LGE GABA 76
25 10 LSX GABA 65
32 15 HY Gnrh1 Glut 57
26 32 OEC 53
31 03 OB-CR Glut 45
1 25 Pineal Glut 36
33 22 MB-HB Sero 28
30 16 HY MM Glut 24

2.3.2 Cell Annotation (High resolution subclass)

MapMyCell Annotation Cell Count (High resolution subclass)
subclass_name count
10 030 L6 CT CTX Glut 2664
6 006 L4/5 IT CTX Glut 2601
69 319 Astro-TE NN 2326
46 016 CA1-ProS Glut 2294
27 017 CA3 Glut 1872
102 318 Astro-NT NN 1568
13 022 L5 ET CTX Glut 1474
4 007 L2/3 IT CTX Glut 1178
64 020 L2/3 IT RSP Glut 1167
29 052 Pvalb Gaba 1020
14 032 L5 NP CTX Glut 909
70 005 L5 IT CTX Glut 872
39 151 TH Prkcd Grin2c Glut 870
8 053 Sst Gaba 817
125 202 PRT Tcf7l2 Gaba 762
25 004 L6 IT CTX Glut 735
24 334 Microglia NN 708
36 326 OPC NN 623
48 327 Oligo NN 571
58 321 Astroependymal NN 536
37 215 SNc-VTA-RAmb Foxa1 Dopa 517
43 046 Vip Gaba 488
94 181 IC Tfap2d Maf Glut 481
55 023 SUB-ProS Glut 480
16 028 L6b/CT ENT Glut 471
38 014 LA-BLA-BMA-PA Glut 434
17 037 DG Glut 417
21 029 L6b CTX Glut 381
159 203 LGv-SPFp-SPFm Nkx2-2 Tcf7l2 Gaba 368
128 168 SPA-SPFm-SPFp-POL-PIL-PoT Sp9 Glut 354
56 021 L4 RSP-ACA Glut 346
23 033 NP SUB Glut 345
72 197 SNr Six3 Gaba 345
142 177 SCig-an-PPT Foxb1 Glut 308
0 047 Sncg Gaba 299
9 049 Lamp5 Gaba 273
132 101 ZI Pax6 Gaba 269
20 009 L2/3 IT PIR-ENTl Glut 261
26 031 CT SUB Glut 260
31 048 RHP-COA Ndnf Gaba 250
97 213 SCsg Gabrr2 Gaba 249
15 001 CLA-EPd-CTX Car3 Glut 246
157 207 SCs Dmbx1 Gaba 194
47 338 Lymphoid NN 193
66 322 Tanycyte NN 187
18 003 L5/6 IT TPE-ENT Glut 184
35 002 IT EP-CLA Glut 178
40 045 OB-STR-CTX Inh IMN 177
12 027 L6b EPd Glut 168
11 013 COAp Grxcr2 Glut 164
134 201 PAG-RN Nkx2-2 Otx1 Gaba 161
120 333 Endo NN 158
28 198 IC Six3 En2 Gaba 155
33 010 IT AON-TT-DP Glut 149
133 331 Peri NN 149
79 204 SC Otx2 Gcnt4 Gaba 144
90 243 PGRN-PARN-MDRN Hoxb5 Glut 144
152 210 PRT Mecom Gaba 143
111 330 VLMC NN 141
65 332 SMC NN 134
50 323 Ependymal NN 128
7 019 L2/3 IT PPP Glut 127
87 199 PAG-MRN-RN Foxa2 Gaba 124
53 285 MY Lhx1 Gly-Gaba 121
22 025 CA2-FC-IG Glut 112
146 209 SCs Pax7 Nfia Gaba 109
149 155 PRC-PAG Pax6 Glut 106
184 172 PAG Pou4f1 Ebf2 Glut 105
80 304 NTS-PARN Neurod2 Gly-Gaba 100
119 195 SNr-VTA Pax5 Npas1 Gaba 97
84 119 SI-MA-LPO-LHA Skor1 Glut 97
91 042 OB-out Frmd7 Gaba 97
176 167 PRC-PAG Tcf7l2 Irx2 Glut 96
101 200 PAG-ND-PCG Onecut1 Gaba 94
141 163 APN C1ql2 Glut 93
124 212 SCs Lef1 Gli3 Gaba 92
165 166 MRN Pou3f1 C1ql4 Glut 92
96 050 Lamp5 Lhx6 Gaba 91
61 034 NP PPP Glut 86
77 214 IPN Otp Crisp1 Gaba 84
274 190 ND-INC Foxd2 Glut 83
117 154 PF Fzd5 Glut 81
51 300 PARN-MDRNd-NTS Gbx2 Gly-Gaba 78
185 174 PAG Pou4f2 Mesi2 Glut 77
86 254 VCO Mafa Meis2 Glut 77
151 308 DCO Il22 Gly-Gaba 77
153 170 PAG-MRN Tfap2b Glut 76
174 187 SCsg Pde5a Glut 74
54 309 CB PLI Gly-Gaba 73
137 165 PAG-MRN Pou3f1 Glut 67
129 164 APN C1ql4 Glut 67
195 089 PVR Six3 Sox3 Gaba 62
41 018 L2 IT PPP-APr Glut 62
178 277 DTN-LDT-IPN Otp Pax3 Gaba 60
93 057 NDB-SI-MA-STRv Lhx8 Gaba 58
181 206 SCm-PAG Cdh23 Gaba 58
189 325 CHOR NN 58
60 336 Monocytes NN 58
167 142 HY Gnrh1 Glut 57
224 173 PAG Pou4f2 Glut 56
156 176 SCig Foxb1 Glut 55
114 141 PH-SUM Foxa1 Glut 55
123 238 NTS Phox2b Glut 55
106 335 BAM NN 54
67 283 PRP Otp Gly-Gaba 54
71 314 CB Granule Glut 54
113 086 MPO-ADP Lhx8 Gaba 53
88 328 OEC NN 53
45 145 MH Tac2 Glut 53
136 169 PAG-SC Pou4f1 Zic1 Glut 52
205 217 PB Lmx1a Glut 51
138 161 PAG Pou4f3 Glut 50
208 102 DMH-LHA Gsx1 Gaba 48
107 222 PB Evx2 Glut 48
168 205 SC-PAG Lef1 Emx2 Gaba 48
49 264 PRNc Otp Gly-Gaba 48
42 237 PRP-NI-PRNc-GRN Otp Glut 47
273 231 IPN-LDT Vsx2 Nkx6-1 Glut 46
92 015 ENTmv-PA-COAp Glut 45
95 263 CS-RPO Meis2 Gaba 44
170 329 ABC NN 44
270 159 IF-RL-CLI-PAG Foxa1 Glut 44
2 056 Sst Chodl Gaba 42
183 180 SCiw Pitx2 Glut 42
243 251 NTS Dbh Glut 41
73 093 RT-ZI Gnb3 Gaba 40
112 098 AHN-SBPV-PVHd Pdrm12 Gaba 40
143 146 LH Pou4f1 Sox1 Glut 39
135 039 OB Meis2 Thsd7b Gaba 38
30 008 L2/3 IT ENT Glut 37
163 228 PSV Pvalb Lhx2 Glut 37
116 147 AD Serpinb7 Glut 37
148 171 PAG Pou4f1 Bnc2 Glut 37
211 211 SC Tnnt1 Gli3 Gaba 36
150 248 MV-SPIV Zic4 Neurod2 Glut 36
1 262 Pineal Crx Glut 36
59 044 OB Dopa-Gaba 36
103 012 MEA Slc17a7 Glut 35
98 311 CBX MLI Megf11 Gaba 35
200 149 PVT-PT Ntrk1 Glut 35
44 282 POR Spp1 Gly-Gaba 35
206 134 PH-ant-LHA Otp Bsx Glut 35
155 246 CU-ECU-SPVI Foxb1 Glut 35
186 312 CBX MLI Cdh22 Gaba 34
63 011 L2 IT ENT-po Glut 33
182 051 Pvalb chandelier Gaba 33
204 247 MV-SPIV Phox2b Ebf3 Lbx1 Glut 33
32 306 SPVI-SPVC Sall3 Lhx1 Gly-Gaba 32
237 097 PVHd-SBPV Six3 Prox1 Gaba 31
199 152 RE-Xi Nox4 Glut 30
52 094 SCH Six6 Cdc14a Gaba 30
223 085 SI-MPO-LPO Lhx8 Gaba 30
108 041 OB-in Frmd7 Gaba 28
179 216 MB-MY Tph2 Glut-Sero 28
110 208 SC Lef1 Otx2 Gaba 28
169 250 CBN Neurod2 Pvalb Glut 27
252 271 NI-RPO Gata3 Nr4a2 Gaba 27
130 279 PSV Pax2 Gly-Gaba 27
177 175 SC Bnc2 Glut 27
260 133 PVH-SO-PVa Otp Glut 25
140 106 PVpo-VMPO-MPN Hmx2 Gaba 25
221 337 DC NN 24
218 035 OB Eomes Ms4a15 Glut 24
162 224 PCG-PRNr Vsx2 Nkx6-1 Glut 24
209 100 AHN Onecut3 Gaba 24
173 287 MV-SPIV-PRP Dmbx1 Gly-Gaba 24
212 109 LGv-ZI Otx2 Gaba 24
164 108 ARH-PVp Tbx3 Gaba 23
62 315 DCO UBC Glut 23
131 313 CBX Purkinje Gaba 23
257 104 TU-ARH Otp Six6 Gaba 23
188 316 Bergmann NN 22
76 038 DG-PIR Ex IMN 22
201 070 LSX Prdm12 Slit2 Gaba 22
158 036 HPF CR Glut 21
81 270 LDT-DTN Gata3 Nfix Gaba 21
175 105 TMd-DMH Foxd2 Gaba 20
126 061 STR D1 Gaba 20
68 114 COAa-PAA-MEA Barhl2 Glut 20
127 156 MB-ant-ve Dmrta2 Glut 19
220 188 SCop Sln Glut 19
139 115 MS-SF Bsx Glut 18
109 317 Astro-CB NN 18
264 305 SPVI-SPVC Sall3 Nfib Gly-Gaba 17
232 196 PAG-PPN Pax5 Sox21 Gaba 17
241 103 PVHd-DMH Lhx6 Gaba 17
233 124 MPN-MPO-PVpo Hmx2 Glut 17
210 160 PAG-SC Neurod2 Meis2 Glut 17
242 132 AHN-RCH-LHA Otp Fezf1 Glut 16
238 268 CS-PRNr-DR En1 Sox2 Gaba 16
171 144 MM Foxb1 Glut 16
191 255 SPVO Mafa Meis2 Glut 16
105 192 PPN-CUN-PCG Otp En1 Gaba 16
118 066 NDB-SI-ant Prdm12 Gaba 16
239 320 Astro-OLF NN 15
160 221 LDT-PCG Vsx2 Lhx4 Glut 15
57 054 STR Prox1 Lhx6 Gaba 14
154 278 NLL Gata3 Gly-Gaba 14
144 139 PH-LHA Foxb1 Glut 14
74 225 PRNc-NI-SG-RPO Vsx2 Nr4a2 Glut 13
213 267 CS-PRNr-PCG Tmem163 Otp Gaba 13
166 117 LHA Barhl2 Glut 13
190 069 LSX Nkx2-1 Gaba 13
254 058 PAL-STR Gaba-Chol 13
180 062 STR D2 Gaba 13
145 083 CEA-BST Rai14 Pdyn Crh Gaba 12
161 296 RPA Pax6 Hoxb5 Gly-Gaba 12
266 107 DMH Hmx2 Gaba 12
34 191 PAG-MRN Rln3 Gaba 12
271 138 PH Pitx2 Glut 12
287 060 OT D3 Folh1 Gaba 12
300 153 MG-POL-SGN Nts Glut 12
236 194 MRN-VTN-PPN Pax5 Cdh23 Gaba 12
249 118 ADP-MPO Trp73 Glut 12
89 065 IA Mgp Gaba 11
258 129 VMH Nr5a1 Glut 11
194 293 PAS-MV Ebf2 Gly-Gaba 11
235 265 PB Sst Gly-Gaba 11
229 140 PMd-LHA Foxb1 Glut 10
3 076 MEA-BST Lhx6 Nfib Gaba 10
245 071 LSX Prdm12 Zeb2 Gaba 10
99 235 PG-TRN-LRN Fat2 Glut 10
225 082 CEA-BST Ebf1 Pdyn Gaba 10
309 186 SCop Pou4f2 Neurod2 Glut 10
255 080 CEA-AAA-BST Six3 Sp9 Gaba 9
248 260 MDRNv Crp Glut 9
247 182 CUN-PPN Evx2 Meis2 Glut 9
240 297 CU-ECU Pax2 Gly-Gaba 9
196 095 DMH Prdm13 Gaba 9
222 272 LDT-PCG-CS Gata3 Lhx1 Gaba 9
214 307 RO-RPA Pkd2l1 Gaba 9
147 162 CUN Evx2 Lhx2 Glut 9
198 290 MY Prox1 Lmo7 Gly-Gaba 9
227 126 ARH-PVp Tbx3 Glut 9
202 276 LDT-PCG St18 Gaba 9
121 143 MM-ant Foxb1 Glut 8
265 055 STR Lhx8 Gaba 8
82 073 MEA-BST Sox6 Gaba 8
187 090 BST-MPN Six3 Nrgn Gaba 8
253 302 MV Xdh Gly-Gaba 8
250 245 SPVI-SPVC Tlx3 Ebf3 Glut 8
192 092 TMv-PMv Tbx3 Hist-Gaba 8
268 059 GPe-SI Sox6 Cyp26b1 Gaba 7
19 099 SBPV-PVa Six6 Satb2 Gaba 7
286 234 MEV Ppp1r1c Glut 7
311 179 SCdg-PAG Tfap2b Glut 7
294 064 STR-PAL Chst9 Gaba 7
207 068 LSX Otx2 Gaba 7
301 157 RN Spp1 Glut 7
85 072 LSX Sall3 Lmo1 Gaba 7
231 310 CBX Golgi Gly-Gaba 7
244 116 AVPV-MEPO-SFO Tbr1 Glut 7
269 026 NLOT Rho Glut 6
277 067 LSX Sall3 Pax6 Gaba 6
217 233 NLL-SOC Spp1 Glut 6
104 063 STR D1 Sema5a Gaba 6
122 284 GRN-IRN-MDRNd Ikzf1 Gly-Gaba 6
197 273 PDTg-PCG Pax6 Gaba 6
296 131 LHA-AHN-PVH Otp Trh Glut 6
261 075 MEA-BST Lhx6 Nr2e1 Gaba 6
272 135 STN-PSTN Pitx2 Glut 6
267 291 NTS-MDRNd Prox1 Zic1 Gly-Gaba 5
78 298 PRP Gata3 Slc6a5 Gly-Gaba 5
293 088 BST Tac2 Gaba 5
306 295 CBN Dmbx1 Gaba 5
297 226 PRNc-PARN Tlx1 Glut 5
5 113 MEA-COA-BMA Ccdc42 Glut 5
298 256 SPVC Mafa Glut 5
230 220 PB Pax5 Glut 5
100 127 DMH-LHA Vgll2 Glut 5
307 185 SCig Tfap2b Chrnb3 Glut 4
281 239 MARN-GRN Pyy Glut 4
282 130 LHA Pmch Glut 4
288 087 MPN-MPO-LPO Lhx6 Zfhx3 Gaba 4
295 193 MRN-PPN-CUN Pax8 Gaba 4
303 150 CM-IAD-CL-PCN Sema5b Glut 4
280 125 DMH Hmx2 Glut 4
203 257 SPVC Ccdc172 Glut 4
234 286 PPY-PGRNl Vip Glyc-Gaba 4
83 281 POR Gata3 Gly-Gaba 4
193 299 MARN-PPY Ngfr Gly-Gaba 4
263 294 MV Pax6 Gly-Gaba 4
262 040 OB Trdn Gaba 4
259 074 MEA-BST Lhx6 Sp9 Gaba 4
215 136 PMv-TMv Pitx2 Glut 4
75 223 B-PB Nr4a2 Glut 4
278 232 LDT Vsx2 Nkx6-1 Nfib Glut 3
279 123 DMH Nkx2-4 Glut 3
285 236 IRN Vip Glut 3
246 091 ARH-PVi Six6 Dopa-Gaba 3
304 280 NLL-po Pax7 Gaba 3
315 112 GPi Tbr1 Cngb3 Gaba-Glut 3
292 122 LHA-MEA Otp Glut 3
216 274 PDTg Otp Shroom3 Gaba 3
319 189 PAG Ucn Glut 2
305 288 MDRN Hoxb5 Ebf2 Gly-Gaba 2
317 240 MDRNv Lhx4 Qrfprl Glut 2
312 178 SCig Foxb1 Otx2 Glut 2
316 184 PAG Tcf24 Glut 2
228 230 PRNr Otp Nfib Glut 2
320 081 ACB-BST-FS D1 Gaba 2
299 043 OB-mi Frmd7 Gaba 2
276 261 HB Calcb Chol 2
226 084 BST-SI-AAA Six3 Slc22a3 Gaba 2
115 292 MV Nkx6-1 Gly-Gaba 2
251 078 SI-MA-ACB Ebf1 Bnc2 Gaba 2
256 120 MEA Otp Foxp2 Glut 2
172 079 CEA-BST Six3 Cyp26b1 Gaba 2
283 219 PB-SUT Tlx3 Lhx2 Glut 2
289 137 PH-an Pitx2 Glut 2
308 258 SPVC Nmu Glut 1
310 218 PSV Lmx1a Trpv6 Glut 1
302 269 LDT Fgf7 Gaba 1
284 275 PDTg Otp Olig3 Gaba 1
313 301 MV Nr4a2 Gly-Gaba 1
314 244 MV-SPIV Slc6a2 Glut 1
219 229 PB-NTS Phox2b Ebf3 Lmx1b Glut 1
290 252 DMX VII Tbx20 Chol 1
318 024 L5 PPP Glut 1
291 183 PBG Mtnr1a Glut-Chol 1
275 242 PGRNd Dmbx1 Glut 1

2.3.3 Spatial cell type (Neurons)

2.3.4 Spatial cell type (Non-Neurons)

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Abbreviation

Cell types & Regions

Astro, Astrocyte;

ABC, arachnoid barrier cells;

BAM, border-associated macrophages;

BLA, Basolateral amygdala;

CB, cerebellum;

CGE, caudal ganglionic eminence;

CHOR, choroid plexus;

CNU, cerebral nuclei;

CR, Cajal–Retzius;

CT, corticothalamic;

CTX, cerebral cortex;

CTXsp, cortical subplate;

DC, dendritic cells;

DCO, dorsal cochlear nucleus;

DG, dentate gyrus;

EA, extended amygdala;

Endo, endothelial cells;

ENT, Entorhinal area;

ENTl, Entorhinal area, lateral part;

Epen, ependymal;

EPI, epithalamus;

ET, extratelencephalic;

GC, granule cell;

HB, hindbrain;

HPF, hippocampal formation;

HY, hypothalamus;

HYa, anterior hypothalamic;

IMN, immature neurons;

IT, intratelencephalic;

L6b, layer 6b;

LGE, lateral ganglionic eminence;

LH, lateral habenula;

LSX, lateral septal complex;

MB, midbrain;

MGE, medial ganglionic eminence;

MH, medial habenula;

MM, medial mammillary nucleus;

MY, medulla;

NN, non-neuronal;

NP, near-projecting;

NT, non-telencephalon;

OB, olfactory bulb;

OEC, olfactory ensheathing cells;

OLF, olfactory areas;

Oligo, oligodendrocytes;

OPC, oligodendrocyte precursor cells;

P, pons;

PAL, pallidum;

Peri, pericytes;

PIR, piriform cortex;

SMC, smooth muscle cells;

STR, striatum;

TE, telencephalon;

TH, thalamus;

UBC, unipolar brush cells;

VLMC, vascular leptomeningeal cells.

Neurotransmitter types

Chol, cholinergic;

Dopa, dopaminergic;

GABA, GABAergic;

Glut, glutamatergic;

Glyc, glycinergic;

Hist, histaminergic;

Nora, noradrenergic;

Sero, serotonergic